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Annual review of physical chemistry最新文献

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Emerging Mechanisms of Metal-Catalyzed RNA and DNA Modifications. 金属催化RNA和DNA修饰的新机制。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-14 DOI: 10.1146/annurev-physchem-082423-030241
Mohd Ahsan, Chinmai Pindi, Giulia Palermo
{"title":"Emerging Mechanisms of Metal-Catalyzed RNA and DNA Modifications.","authors":"Mohd Ahsan, Chinmai Pindi, Giulia Palermo","doi":"10.1146/annurev-physchem-082423-030241","DOIUrl":"10.1146/annurev-physchem-082423-030241","url":null,"abstract":"<p><p>Metal ions play a critical role in various chemical, biological, and environmental processes. This review reports on emerging chemical mechanisms in the catalysis of DNA and RNA. We provide an overview of the metal-dependent mechanisms of DNA cleavage in CRISPR (clustered regularly interspaced short palindromic repeats)-Cas systems that are transforming life sciences through genome editing technologies, and showcase intriguing metal-dependent mechanisms of RNA cleavages. We show that newly discovered CRISPR-Cas complexes operate as protein-assisted ribozymes, highlighting RNA's versatility and the enhancement of CRISPR-Cas functions through strategic metal ion use. We demonstrate the power of computer simulations in observing chemical processes as they unfold and in advancing structural biology through innovative approaches for refining cryo-electron microscopy maps. Understanding metal ion involvement in nucleic acid catalysis is crucial for advancing genome editing, aiding therapeutic interventions for genetic disorders, and improving the editing tools' specificity and efficiency.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":" ","pages":"497-518"},"PeriodicalIF":11.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structure-Photophysical Property Relationships in Noncanonical and Synthetic Nucleobases. 非规范和合成核碱基的结构-光物理性质关系。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-14 DOI: 10.1146/annurev-physchem-082423-022427
Sean J Hoehn, Sarah E Krul, Sourav Kanti Seth, Carlos E Crespo-Hernández
{"title":"Structure-Photophysical Property Relationships in Noncanonical and Synthetic Nucleobases.","authors":"Sean J Hoehn, Sarah E Krul, Sourav Kanti Seth, Carlos E Crespo-Hernández","doi":"10.1146/annurev-physchem-082423-022427","DOIUrl":"10.1146/annurev-physchem-082423-022427","url":null,"abstract":"<p><p>This review provides focused coverage of the photophysical properties of noncanonical and synthetic nucleobases reported over the past decade. It emphasizes key research findings and physical insights gathered for prebiotic and fluorescent nucleobase analogs, sulfur- and selenium-substituted nucleobases, aza-substituted nucleobases, epigenetic nucleobases and their oxidation products, and nucleobases utilized for expanding DNA/RNA to reveal central structure-photophysical property relationships. Further research and development in this emerging field, coupled with machine learning methods, will enable the effective harnessing of nucleobases' modifications for applications in biotechnology, biomedicine, therapeutics, and even the creation of live semisynthetic organisms.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":" ","pages":"539-564"},"PeriodicalIF":11.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424553","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Variational Path Sampling of Rare Dynamical Events. 稀有动力事件的变分路径抽样。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-19 DOI: 10.1146/annurev-physchem-083122-115001
Aditya N Singh, Avishek Das, David T Limmer
{"title":"Variational Path Sampling of Rare Dynamical Events.","authors":"Aditya N Singh, Avishek Das, David T Limmer","doi":"10.1146/annurev-physchem-083122-115001","DOIUrl":"10.1146/annurev-physchem-083122-115001","url":null,"abstract":"<p><p>This article reviews the concepts and methods of variational path sampling. These methods allow computational studies of rare events in systems driven arbitrarily far from equilibrium. Based upon a statistical mechanics of trajectory space and leveraging the theory of large deviations, they provide a perspective from which dynamical phenomena can be studied with the same types of ensemble reweighting ideas that have been used for static equilibrium properties. Applications to chemical, material, and biophysical systems are highlighted.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":" ","pages":"639-662"},"PeriodicalIF":11.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Ultrafast Spectroscopy and Dynamics of Photoredox Catalysis. 光氧化催化的超快光谱学和动力学。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-03 DOI: 10.1146/annurev-physchem-082423-013952
John D Sakizadeh, Rachel Weiss, Gregory D Scholes, Bryan Kudisch
{"title":"Ultrafast Spectroscopy and Dynamics of Photoredox Catalysis.","authors":"John D Sakizadeh, Rachel Weiss, Gregory D Scholes, Bryan Kudisch","doi":"10.1146/annurev-physchem-082423-013952","DOIUrl":"10.1146/annurev-physchem-082423-013952","url":null,"abstract":"<p><p>Photoredox catalysis has emerged as a powerful platform for chemical synthesis, utilizing chromophore excited states as selective energy stores to surmount chemical activation barriers toward making desirable products. Developments in this field have pushed synthetic chemists to design and discover new photocatalysts with novel and impactful photoreactivity but also with uncharacterized excited states and only an approximate mechanistic understanding. This review highlights specific instances in which ultrafast spectroscopies dissected the photophysical and photochemical dynamics of new classes of photoredox catalysts and their photochemical reactions. After briefly introducing the photophysical processes and ultrafast spectroscopic methods central to this topic, the review describes selected recent examples that evoke distinct classes of photoredox catalysts with demonstrated synthetic utility and ultrafast spectroscopic characterization. This review cements the significant role of ultrafast spectroscopy in modern photocatalyzed organic transformations and institutionalizes the developing intersection of synthetic organic chemistry and physical chemistry.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":" ","pages":"203-229"},"PeriodicalIF":11.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143122001","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Nonadiabatic Dynamics with the Mapping Approach to Surface Hopping (MASH). 非绝热动力学与表面跳跃（MASH）的映射方法。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-19 DOI: 10.1146/annurev-physchem-082423-120631
Jeremy O Richardson, Joseph E Lawrence, Jonathan R Mannouch
{"title":"Nonadiabatic Dynamics with the Mapping Approach to Surface Hopping (MASH).","authors":"Jeremy O Richardson, Joseph E Lawrence, Jonathan R Mannouch","doi":"10.1146/annurev-physchem-082423-120631","DOIUrl":"10.1146/annurev-physchem-082423-120631","url":null,"abstract":"<p><p>The mapping approach to surface hopping (MASH) combines the rigor of quasiclassical mapping approaches with the pragmatism of surface hopping to obtain a practical trajectory-based method for simulating nonadiabatic dynamics in molecular systems. In this review, we outline the derivation of MASH, prove a number of important properties that ensure its reliability, and illustrate its accuracy for computing nonadiabatic rate constants as well as ultrafast photochemical dynamics.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":" ","pages":"663-687"},"PeriodicalIF":11.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cellular Signaling at the Nano-Bio Interface: Spotlighting Membrane Curvature. 细胞信号在纳米生物界面：聚光灯膜曲率。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2025-04-01 DOI: 10.1146/annurev-physchem-090722-021151
Chih-Hao Lu, Christina E Lee, Melissa L Nakamoto, Bianxiao Cui
{"title":"Cellular Signaling at the Nano-Bio Interface: Spotlighting Membrane Curvature.","authors":"Chih-Hao Lu, Christina E Lee, Melissa L Nakamoto, Bianxiao Cui","doi":"10.1146/annurev-physchem-090722-021151","DOIUrl":"https://doi.org/10.1146/annurev-physchem-090722-021151","url":null,"abstract":"<p><p>No longer viewed as a passive consequence of cellular activities, membrane curvature-the physical shape of the cell membrane-is now recognized as an active constituent of biological processes. Nanoscale topographies on extracellular matrices or substrate surfaces impart well-defined membrane curvatures on the plasma membrane. This review examines biological events occurring at the nano-bio interface, the physical interface between the cell membrane and surface nanotopography, which activates intracellular signaling by recruiting curvature-sensing proteins. We encompass a wide range of biological processes at the nano-bio interface, including cell adhesion, endocytosis, glycocalyx redistribution, regulation of mechanosensitive ion channels, cell migration, and differentiation. Despite the diversity of processes, we call attention to the critical role of membrane curvature in each process. We particularly highlight studies that elucidate molecular mechanisms involving curvature-sensing proteins with the hope of providing comprehensive insights into this rapidly advancing area of research.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"76 1","pages":"251-277"},"PeriodicalIF":11.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12043246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143961310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Electric Fields at Solid-Liquid Interfaces: Insights from Molecular Dynamics Simulation. 固-液界面的电场：分子动力学模拟的启示。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-03 DOI: 10.1146/annurev-physchem-082820-112101
Julia A Nauman, Dylan Suvlu, Adam P Willard
{"title":"Electric Fields at Solid-Liquid Interfaces: Insights from Molecular Dynamics Simulation.","authors":"Julia A Nauman, Dylan Suvlu, Adam P Willard","doi":"10.1146/annurev-physchem-082820-112101","DOIUrl":"10.1146/annurev-physchem-082820-112101","url":null,"abstract":"<p><p>In this review, we explore the electrostatic environment of the interface between a solid and dilute electrolyte solution, with an emphasis on the electric field profiles that these systems produce. We review the theoretical formalism that connects electrostatic potential profiles, electric field profiles, and charge density fields. This formalism has served as the basis for our understanding of interfacial electric fields and their influences on microscopic chemical and physical processes. Comparing various traditional models of interfacial electrostatics to the results of molecular dynamics (MD) simulation yields mutually inconsistent descriptions of the interfacial electric field profile. We present MD simulation results demonstrating that the average electric field profiles experienced by particles at the interface differ from the properties of traditional models and from the fields derived from the mean charge density of atomistic simulations. Furthermore, these experienced electric field profiles are species-dependent. Based on these results, we assert that a single unifying electrostatic potential profile-the gradient of which defines a single unifying electric field profile-cannot correctly predict the electrostatic forces that act on species at the interface.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":" ","pages":"181-202"},"PeriodicalIF":11.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143121995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Hydrogen-Bonding Motifs in Hydroxy-Functionalized Ionic Liquids. 羟基功能化离子液体中的氢键基序。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2025-04-01 DOI: 10.1146/annurev-physchem-082423-020307
Anne Strate, Dietmar Paschek, Ralf Ludwig
{"title":"Hydrogen-Bonding Motifs in Hydroxy-Functionalized Ionic Liquids.","authors":"Anne Strate, Dietmar Paschek, Ralf Ludwig","doi":"10.1146/annurev-physchem-082423-020307","DOIUrl":"https://doi.org/10.1146/annurev-physchem-082423-020307","url":null,"abstract":"<p><p>The unique properties of ionic liquids (ILs) result from the tunable mélange of Coulomb interactions, hydrogen bonding, and dispersion interactions among the constituent ions. In hydroxy-functionalized ILs, local and directional hydrogen bonds (H-bonds) lead to the anticipated formation of ion pairs but also to the elusive formation of cationic clusters. Here, we review how hydrogen-bonding motifs in the bulk liquid and gas phase of hydroxy-functionalized ILs shed light on the general nature of hydrogen bonding. Infrared spectroscopy, nuclear magnetic resonance, neutron diffraction, and molecular dynamics simulations provide information about the structure, strength, and dynamics of cationic clusters in the bulk liquid ILs. Cryogenic ion vibrational predissociation (CIVP) spectroscopy along with density functional theory calculations has established a clear picture about the specific contacts within isolated H-bonded cationic clusters formed in the gas phase. This information from experiment, simulation, and theory provides a fundamental understanding of hydrogen bonding between the ions in ILs.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":"76 1","pages":"589-614"},"PeriodicalIF":11.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143974313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Organization and Dynamics of Chromosomes. 染色体的组织与动力学。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2025-04-01 Epub Date: 2025-02-19 DOI: 10.1146/annurev-physchem-082423-024123
D Thirumalai, Guang Shi, Sucheol Shin, Changbong Hyeon
{"title":"Organization and Dynamics of Chromosomes.","authors":"D Thirumalai, Guang Shi, Sucheol Shin, Changbong Hyeon","doi":"10.1146/annurev-physchem-082423-024123","DOIUrl":"10.1146/annurev-physchem-082423-024123","url":null,"abstract":"<p><p>How long thread-like eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which reproduce contact maps that measure the probabilities that two loci are in spatial contact, have predicted the 3D structures of interphase chromosomes. Data-driven approaches, using contact maps as input, predict that mitotic helical chromosomes are characterized by a switch in handedness, referred to as perversion. By using experimentally derived effective interactions between chromatin loci in simulations, structures of conventional and inverted nuclei have been accurately predicted. Polymer theory and simulations show that the dynamics of individual loci in chromatin exhibit subdiffusive behavior but the diffusion exponents are broadly distributed, which accords well with experiments. Although coarse-grained models are successful, many challenging problems remain, which require the creation of new experimental and computational tools to understand genome biology.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":" ","pages":"565-588"},"PeriodicalIF":11.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reinvented: An Attosecond Chemist. 重新发明:阿秒化学家。
IF 11.7 1区 化学
Annual review of physical chemistry Pub Date : 2024-06-01 Epub Date: 2024-06-14 DOI: 10.1146/annurev-physchem-083122-011610
Stephen R Leone
{"title":"Reinvented: An Attosecond Chemist.","authors":"Stephen R Leone","doi":"10.1146/annurev-physchem-083122-011610","DOIUrl":"10.1146/annurev-physchem-083122-011610","url":null,"abstract":"<p><p>Attosecond science requires a substantial rethinking of how to make measurements on very short timescales; how to acquire the necessary equipment, technology, and personnel; and how to build a set of laboratories for such experiments. This entails a rejuvenation of the author in many respects, in the laboratory itself, with regard to students and postdocs, and in generating funding for research. It also brings up questions of what it means to do attosecond science, and the discovery of the power of X-ray spectroscopy itself, which complements the short timescales addressed. The lessons learned, expressed in the meanderings of this autobiographical article, may be of benefit to others who try to reinvent themselves.</p>","PeriodicalId":7967,"journal":{"name":"Annual review of physical chemistry","volume":" ","pages":"1-19"},"PeriodicalIF":11.7,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138443588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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